#include "readtree.h"
+/***********************************************************************/
+//Parent Class
+// The following functions are used by all reading formats.
+/***********************************************************************/
+ReadTree::ReadTree() {
+ try {
+ globaldata = GlobalData::getInstance();
+ T = new Tree();
+ numNodes = T->getNumNodes();
+ numLeaves = T->getNumLeaves();
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadTree class function ReadTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************************/
+int ReadTree::readSpecialChar(istream& f, char c, string name) {
+ try {
+ char d;
+
+ while(isspace(d=f.get())) {;}
+ if(d == EOF){
+ cerr << "Error: Input file ends prematurely, expecting a " << name << "\n";
+ exit(1);
+ }
+ if(d != c){
+ cerr << "Error: Expected " << name << " in input file. Found " << d << ".\n";
+ exit(1);
+ }
+ if(d == ')' && f.peek() == '\n'){
+ while(isspace(d=f.get())) {;}
+ f.putback(d);
+ }
+
+ return d;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadTree class function readSpecialChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int ReadTree::readNodeChar(istream& f) {
+ try {
+ char d;
+ while(isspace(d=f.get())) {;}
+ if(d == EOF){
+ cerr << "Error: Input file ends prematurely, expecting a left parenthesis\n";
+ exit(1);
+ }
+ return d;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadTree class function readNodeChar. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+float ReadTree::readBranchLength(istream& f) {
+ try {
+ float b;
+
+ if(!(f >> b)){
+ cerr << "Error: Missing branch length in input tree.\n";
+ exit(1);
+ }
+
+ return b;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadTree class Function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadTree class function readBranchLength. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+
+/***********************************************************************/
+/***********************************************************************/
+
+
+//Child Classes Below
+
+/***********************************************************************/
+/***********************************************************************/
+//This class reads a file in Newick form and stores it in a tree.
+
+void ReadNewickTree::read() {
+ try {
+ int n = 0;
+ int lc, rc;
+
+ int rooted = 0;
+
+ int ch = filehandle.peek();
+
+ if(ch == '('){
+ n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
+ lc = readNewickInt(filehandle, n, T);
+
+ if(filehandle.peek()==','){
+ readSpecialChar(filehandle,',',"comma");
+ }
+ // ';' means end of tree.
+ else if((ch=filehandle.peek())==';' || ch=='['){
+ rooted = 1;
+ }
+ if(rooted != 1){
+ rc = readNewickInt(filehandle, n, T);
+ if(filehandle.peek() == ')'){
+ readSpecialChar(filehandle,')',"right parenthesis");
+ }
+ }
+ }
+ //note: treeclimber had the code below added - not sure why?
+ else{
+ filehandle.putback(ch);
+ char name[MAX_LINE];
+ filehandle.get(name, MAX_LINE,'\n');
+ SKIPLINE(filehandle, ch);
+
+
+ n = T->getIndex(name);
+ if(n!=0){
+ cerr << "Internal error: The only taxon is not taxon 0.\n";
+ exit(1);
+ }
+ lc = rc = -1;
+ }
+
+ while((ch=filehandle.get())!=';'){;}
+ if(rooted != 1){
+ T->tree[n].setChildren(lc,rc);
+ T->tree[n].setBranchLength(0);
+ T->tree[n].setParent(-1);
+ if(lc!=-1){ T->tree[lc].setParent(n); }
+ if(rc!=-1){ T->tree[rc].setParent(n); }
+ }
+
+ //save tree for later commands
+ globaldata->gTree = T;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadNewickTree class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
+ try {
+ int c = readNodeChar(f);
+
+ if(c == '('){
+ int lc = readNewickInt(f, n, T);
+ readSpecialChar(f,',',"comma");
+
+ int rc = readNewickInt(f, n, T);
+ if(f.peek()==')'){
+ readSpecialChar(f,')',"right parenthesis");
+ }
+
+ if(f.peek() == ':'){
+ readSpecialChar(f,':',"colon");
+ if(n >= numNodes){ cerr << "Error: Too many nodes in input tree\n"; exit(1); }
+ T->tree[n].setBranchLength(readBranchLength(f));
+ }else{T->tree[n].setBranchLength(0.0); }
+
+ T->tree[n].setChildren(lc,rc);
+ T->tree[lc].setParent(n);
+ T->tree[rc].setParent(n);
+
+ return n++;
+ }else{
+ f.putback(c);
+ string name = "";
+ char d=f.get();
+ while(d != ':' && d != ',' && d!=')' && d!='\n'){
+ name += d;
+ d=f.get();
+ }
+
+ int blen = 0;
+ if(d == ':') { blen = 1; }
+
+ f.putback(d);
+
+ //set group info
+ string group = globaldata->gTreemap->getGroup(name);
+
+ //find index in tree of name
+ int n1 = T->getIndex(name);
+
+ if(n1 == -1){cerr << "Name: " << name << " not found\n"; exit(1);}
+
+ else T->tree[n1].setGroup(group);
+
+ T->tree[n1].setChildren(-1,-1);
+
+ if(blen == 1){
+ f.get();
+ T->tree[n1].setBranchLength(readBranchLength(f));
+ }else{
+ T->tree[n1].setBranchLength(0.0);
+ }
+
+ while((c=f.get())!=0 && (c != ':' && c != ',' && c!=')') ) {;}
+ f.putback(c);
+
+ return n1;
+ }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the ReadNewickTree class function readNewickInt. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+/**************************************************************************************************/
+
\ No newline at end of file
projects / mothur.git / blobdiff